“Unix and Perl Primer for Biologists” by Keith Bradnam and Ian Korf.

http://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v3.0.html

This site provides a gentle and structured introduction to Unix and Perl programming geared specifically for biologists.  It includes several exercises to get beginners comfortable with working with commonly used commands.  I haven’t used it in teaching yet, but found it very helpful myself!

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